sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.180 Å
X-ray
2011-05-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.720 | 6.720 | 6.720 | 0.000 | 6.720 | 1 |
| Name: | Glucokinase |
|---|---|
| ID: | HXK4_HUMAN |
| AC: | P35557 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.764 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.472 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 68.09 | 31.91 |
| According to VolSite | |
| HET Code: | S41 |
|---|---|
| Formula: | C22H20N6O4 |
| Molecular weight: | 432.432 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.62 % |
| Polar Surface area: | 123.34 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -8.38872 | 2.26381 | 19.4346 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C6 | CG1 | VAL- 62 | 3.57 | 0 | Hydrophobic |
| N14 | O | ARG- 63 | 3.08 | 163.51 | H-Bond (Ligand Donor) |
| N27 | N | ARG- 63 | 3.02 | 169.8 | H-Bond (Protein Donor) |
| C5 | CG2 | THR- 65 | 4.34 | 0 | Hydrophobic |
| C32 | CG2 | ILE- 159 | 3.98 | 0 | Hydrophobic |
| C10 | CE | MET- 210 | 4.03 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 211 | 4.05 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 211 | 3.58 | 0 | Hydrophobic |
| C10 | CD1 | TYR- 214 | 3.79 | 0 | Hydrophobic |
| C10 | CG | GLU- 221 | 3.75 | 0 | Hydrophobic |
| C10 | CG | MET- 235 | 3.55 | 0 | Hydrophobic |
| C32 | CB | ALA- 456 | 4.29 | 0 | Hydrophobic |
